Does anyone have any experience with the RPKM (reads per kilobase of exon per million mapped reads) as calculated by TopHat? I can't find any documentation on how this is calculated, and I'm trying to make sure that it standardizes for the total number of mapped reads (as suggested by the name of the metric). I would like to compare RPKM values between samples which have different numbers of total reads and mapped reads, and I'm wondering if I need to do my own standardization for the total number of mapped reads or if this is unnecessary because TopHat has already corrected for it.
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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